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Protein

Protocadherin-12

Gene

PCDH12

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Cellular adhesion molecule that may play an important role in cell-cell interactions at interendothelial junctions. Promotes homotypic calcium-dependent aggregation and adhesion and clusters at intercellular junctions. Unable to bind to catenins, weakly associates with the cytoskeleton (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Cell adhesion

Keywords - Ligandi

Calcium

Names & Taxonomyi

Protein namesi
Recommended name:
Protocadherin-12
Alternative name(s):
Vascular cadherin-2
Vascular endothelial cadherin-2
Short name:
VE-cad-2
Short name:
VE-cadherin-2
Gene namesi
Name:PCDH12
ORF Names:UNQ395/PRO731
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 5

Organism-specific databases

HGNCiHGNC:8657. PCDH12.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini25 – 718694ExtracellularSequence analysisAdd
BLAST
Transmembranei719 – 73921HelicalSequence analysisAdd
BLAST
Topological domaini740 – 1184445CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

  • cell-cell junction Source: Ensembl
  • extracellular exosome Source: UniProtKB
  • integral component of plasma membrane Source: ProtInc
  • plasma membrane Source: ProtInc
Complete GO annotation...

Keywords - Cellular componenti

Cell junction, Cell membrane, Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA32998.

Polymorphism and mutation databases

BioMutaiPCDH12.
DMDMi22095989.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2424Sequence analysisAdd
BLAST
Chaini25 – 11841160Protocadherin-12PRO_0000003996Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi415 – 4151N-linked (GlcNAc...)Sequence analysis
Glycosylationi582 – 5821N-linked (GlcNAc...)Sequence analysis
Glycosylationi659 – 6591N-linked (GlcNAc...)Sequence analysis
Glycosylationi662 – 6621N-linked (GlcNAc...)Sequence analysis
Modified residuei859 – 8591PhosphoserineBy similarity
Modified residuei1062 – 10621PhosphoserineCombined sources

Keywords - PTMi

Glycoprotein, Phosphoprotein

Proteomic databases

PaxDbiQ9NPG4.
PRIDEiQ9NPG4.

PTM databases

iPTMnetiQ9NPG4.
PhosphoSiteiQ9NPG4.

Expressioni

Tissue specificityi

Expressed in highly vascularized tissues including the heart and placenta, but most tissues contain a low level of expression. Prominent expression in the spleen.

Gene expression databases

BgeeiQ9NPG4.
CleanExiHS_PCDH12.
ExpressionAtlasiQ9NPG4. baseline and differential.
GenevisibleiQ9NPG4. HS.

Organism-specific databases

HPAiHPA051242.

Interactioni

Protein-protein interaction databases

BioGridi119445. 17 interactions.
DIPiDIP-47292N.
IntActiQ9NPG4. 2 interactions.
STRINGi9606.ENSP00000231484.

Structurei

3D structure databases

ProteinModelPortaliQ9NPG4.
SMRiQ9NPG4. Positions 31-683.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini28 – 135108Cadherin 1PROSITE-ProRule annotationAdd
BLAST
Domaini136 – 244109Cadherin 2PROSITE-ProRule annotationAdd
BLAST
Domaini245 – 352108Cadherin 3PROSITE-ProRule annotationAdd
BLAST
Domaini355 – 460106Cadherin 4PROSITE-ProRule annotationAdd
BLAST
Domaini461 – 565105Cadherin 5PROSITE-ProRule annotationAdd
BLAST
Domaini600 – 711112Cadherin 6PROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi1177 – 11815Poly-Ser

Sequence similaritiesi

Contains 6 cadherin domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG3594. Eukaryota.
ENOG410XQHI. LUCA.
GeneTreeiENSGT00840000129695.
HOVERGENiHBG101142.
InParanoidiQ9NPG4.
KOiK16499.
OMAiWELEIVV.
OrthoDBiEOG7J445X.
PhylomeDBiQ9NPG4.
TreeFamiTF352008.

Family and domain databases

Gene3Di2.60.40.60. 6 hits.
InterProiIPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR020894. Cadherin_CS.
IPR013164. Cadherin_N.
IPR030720. Protocadherin-12.
[Graphical view]
PANTHERiPTHR24028:SF42. PTHR24028:SF42. 3 hits.
PfamiPF00028. Cadherin. 5 hits.
PF08266. Cadherin_2. 1 hit.
[Graphical view]
PRINTSiPR00205. CADHERIN.
SMARTiSM00112. CA. 6 hits.
[Graphical view]
SUPFAMiSSF49313. SSF49313. 5 hits.
PROSITEiPS00232. CADHERIN_1. 5 hits.
PS50268. CADHERIN_2. 6 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q9NPG4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMQLLQLLLG LLGPGGYLFL LGDCQEVTTL TVKYQVSEEV PSGTVIGKLS
60 70 80 90 100
QELGREERRR QAGAAFQVLQ LPQALPIQVD SEEGLLSTGR RLDREQLCRQ
110 120 130 140 150
WDPCLVSFDV LATGDLALIH VEIQVLDIND HQPRFPKGEQ ELEISESASL
160 170 180 190 200
RTRIPLDRAL DPDTGPNTLH TYTLSPSEHF ALDVIVGPDE TKHAELIVVK
210 220 230 240 250
ELDREIHSFF DLVLTAYDNG NPPKSGTSLV KVNVLDSNDN SPAFAESSLA
260 270 280 290 300
LEIQEDAAPG TLLIKLTATD PDQGPNGEVE FFLSKHMPPE VLDTFSIDAK
310 320 330 340 350
TGQVILRRPL DYEKNPAYEV DVQARDLGPN PIPAHCKVLI KVLDVNDNIP
360 370 380 390 400
SIHVTWASQP SLVSEALPKD SFIALVMADD LDSGHNGLVH CWLSQELGHF
410 420 430 440 450
RLKRTNGNTY MLLTNATLDR EQWPKYTLTL LAQDQGLQPL SAKKQLSIQI
460 470 480 490 500
SDINDNAPVF EKSRYEVSTR ENNLPSLHLI TIKAHDADLG INGKVSYRIQ
510 520 530 540 550
DSPVAHLVAI DSNTGEVTAQ RSLNYEEMAG FEFQVIAEDS GQPMLASSVS
560 570 580 590 600
VWVSLLDAND NAPEVVQPVL SDGKASLSVL VNASTGHLLV PIETPNGLGP
610 620 630 640 650
AGTDTPPLAT HSSRPFLLTT IVARDADSGA NGEPLYSIRS GNEAHLFILN
660 670 680 690 700
PHTGQLFVNV TNASSLIGSE WELEIVVEDQ GSPPLQTRAL LRVMFVTSVD
710 720 730 740 750
HLRDSARKPG ALSMSMLTVI CLAVLLGIFG LILALFMSIC RTEKKDNRAY
760 770 780 790 800
NCREAESTYR QQPKRPQKHI QKADIHLVPV LRGQAGEPCE VGQSHKDVDK
810 820 830 840 850
EAMMEAGWDP CLQAPFHLTP TLYRTLRNQG NQGAPAESRE VLQDTVNLLF
860 870 880 890 900
NHPRQRNASR ENLNLPEPQP ATGQPRSRPL KVAGSPTGRL AGDQGSEEAP
910 920 930 940 950
QRPPASSATL RRQRHLNGKV SPEKESGPRQ ILRSLVRLSV AAFAERNPVE
960 970 980 990 1000
ELTVDSPPVQ QISQLLSLLH QGQFQPKPNH RGNKYLAKPG GSRSAIPDTD
1010 1020 1030 1040 1050
GPSARAGGQT DPEQEEGPLD PEEDLSVKQL LEEELSSLLD PSTGLALDRL
1060 1070 1080 1090 1100
SAPDPAWMAR LSLPLTTNYR DNVISPDAAA TEEPRTFQTF GKAEAPELSP
1110 1120 1130 1140 1150
TGTRLASTFV SEMSSLLEML LEQRSSMPVE AASEALRRLS VCGRTLSLDL
1160 1170 1180
ATSAASGMKV QGDPGGKTGT EGKSRGSSSS SRCL
Length:1,184
Mass (Da):128,995
Last modified:October 1, 2000 - v1
Checksum:i45314473DC503E8D
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti385 – 3862HN → KD in BAB55016 (PubMed:14702039).Curated
Sequence conflicti389 – 3902VH → LG in BAB55016 (PubMed:14702039).Curated
Sequence conflicti442 – 4421A → V in BAB14677 (PubMed:14702039).Curated
Sequence conflicti753 – 7531R → W in BAB14677 (PubMed:14702039).Curated
Sequence conflicti814 – 8141A → T in BAB14837 (PubMed:14702039).Curated
Sequence conflicti970 – 9701H → Y in BAB14837 (PubMed:14702039).Curated
Sequence conflicti1051 – 10511S → C in BAB14677 (PubMed:14702039).Curated
Sequence conflicti1181 – 11811S → SSSS in BAB14837 (PubMed:14702039).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti385 – 3851H → N.1 Publication
Corresponds to variant rs164075 [ dbSNP | Ensembl ].
VAR_020368
Natural varianti640 – 6401S → N.2 Publications
Corresponds to variant rs164515 [ dbSNP | Ensembl ].
VAR_020369

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF231025 mRNA. Translation: AAF61931.1.
AF240635 mRNA. Translation: AAF73962.1.
AB026893 mRNA. Translation: BAA95162.1.
AK023785 mRNA. Translation: BAB14677.1.
AK024140 mRNA. Translation: BAB14837.1.
AK027282 mRNA. Translation: BAB55016.1.
AY358428 mRNA. Translation: AAQ88794.1.
CCDSiCCDS4269.1.
RefSeqiNP_057664.1. NM_016580.3.
UniGeneiHs.439474.
Hs.600230.

Genome annotation databases

EnsembliENST00000231484; ENSP00000231484; ENSG00000113555.
GeneIDi51294.
KEGGihsa:51294.
UCSCiuc003llx.4. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF231025 mRNA. Translation: AAF61931.1.
AF240635 mRNA. Translation: AAF73962.1.
AB026893 mRNA. Translation: BAA95162.1.
AK023785 mRNA. Translation: BAB14677.1.
AK024140 mRNA. Translation: BAB14837.1.
AK027282 mRNA. Translation: BAB55016.1.
AY358428 mRNA. Translation: AAQ88794.1.
CCDSiCCDS4269.1.
RefSeqiNP_057664.1. NM_016580.3.
UniGeneiHs.439474.
Hs.600230.

3D structure databases

ProteinModelPortaliQ9NPG4.
SMRiQ9NPG4. Positions 31-683.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119445. 17 interactions.
DIPiDIP-47292N.
IntActiQ9NPG4. 2 interactions.
STRINGi9606.ENSP00000231484.

PTM databases

iPTMnetiQ9NPG4.
PhosphoSiteiQ9NPG4.

Polymorphism and mutation databases

BioMutaiPCDH12.
DMDMi22095989.

Proteomic databases

PaxDbiQ9NPG4.
PRIDEiQ9NPG4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000231484; ENSP00000231484; ENSG00000113555.
GeneIDi51294.
KEGGihsa:51294.
UCSCiuc003llx.4. human.

Organism-specific databases

CTDi51294.
GeneCardsiPCDH12.
HGNCiHGNC:8657. PCDH12.
HPAiHPA051242.
MIMi605622. gene.
neXtProtiNX_Q9NPG4.
PharmGKBiPA32998.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3594. Eukaryota.
ENOG410XQHI. LUCA.
GeneTreeiENSGT00840000129695.
HOVERGENiHBG101142.
InParanoidiQ9NPG4.
KOiK16499.
OMAiWELEIVV.
OrthoDBiEOG7J445X.
PhylomeDBiQ9NPG4.
TreeFamiTF352008.

Miscellaneous databases

ChiTaRSiPCDH12. human.
GeneWikiiPCDH12.
GenomeRNAii51294.
NextBioi54569.
PROiQ9NPG4.
SOURCEiSearch...

Gene expression databases

BgeeiQ9NPG4.
CleanExiHS_PCDH12.
ExpressionAtlasiQ9NPG4. baseline and differential.
GenevisibleiQ9NPG4. HS.

Family and domain databases

Gene3Di2.60.40.60. 6 hits.
InterProiIPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR020894. Cadherin_CS.
IPR013164. Cadherin_N.
IPR030720. Protocadherin-12.
[Graphical view]
PANTHERiPTHR24028:SF42. PTHR24028:SF42. 3 hits.
PfamiPF00028. Cadherin. 5 hits.
PF08266. Cadherin_2. 1 hit.
[Graphical view]
PRINTSiPR00205. CADHERIN.
SMARTiSM00112. CA. 6 hits.
[Graphical view]
SUPFAMiSSF49313. SSF49313. 5 hits.
PROSITEiPS00232. CADHERIN_1. 5 hits.
PS50268. CADHERIN_2. 6 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes."
    Wu Q., Maniatis T.
    Proc. Natl. Acad. Sci. U.S.A. 97:3124-3129(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "cDNA cloning, chromosomal mapping, and expression analysis of human VE-cadherin-2."
    Ludwig D., Lorenz J., Dejana E., Bohlen P., Hicklin D.J., Witte L., Pytowski B.
    Mamm. Genome 11:1030-1033(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Fetal kidney.
  3. "Human vascular cadherin-2."
    Seki N., Hattori A., Hayashi A., Kozuma S., Muramatsu M., Saito T.
    Submitted (APR-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  4. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANTS ASN-385 AND ASN-640.
    Tissue: Embryo and Placenta.
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT ASN-640.
  6. "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome."
    Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., Ye M., Zou H.
    J. Proteomics 96:253-262(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1062, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.

Entry informationi

Entry nameiPCD12_HUMAN
AccessioniPrimary (citable) accession number: Q9NPG4
Secondary accession number(s): Q6UXB6
, Q96KB8, Q9H7Y6, Q9H8E0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 2, 2002
Last sequence update: October 1, 2000
Last modified: May 11, 2016
This is version 132 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 5
    Human chromosome 5: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.